Introduction to Bioinformatics - Module 2
All commands so far are technically programs on their own.
ls, cat, head, etc
Other programs can also be installed and run from the command line
Why Use a Package Manager?
Efficiency: automate handling of software packages, no manual installations and updates
Dependency Resolution: manage dependencies
sudo apt install firefox
sudo: grants permission to make changes on your computer. Ensures necessary authority to modify system settings and files. Requires your password
On macOS, Homebrew is a popular package manager
Homebrew simplifies the installation of software on macOS
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
Once Homebrew is installed, you can use it to install packages
brew install bcftools
brew install tabix
Homebrew will handle dependencies and set up the programs for you
man unzip
man unzip
unzip -h
unzip -h
Use command line option -h
unzip my_compressed_files.zip -d my_files/